Open loguille opened 1 month ago
I met the similar error today.
(scRNA) leiyao@ProfWLYangLabServer:/mnt/Extend1/leiyao/20240716_JN_SLEscRNA$ bash 01.test.sh
N E X T F L O W ~ version 24.04.3
Launching `https://github.com/nf-core/scrnaseq` [compassionate_borg] DSL2 - revision: c8f02f515d [master]
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,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/scrnaseq v2.7.0-gc8f02f5
------------------------------------------------------
Core Nextflow options
revision : master
runName : compassionate_borg
containerEngine: singularity
launchDir : /mnt/Extend1/leiyao/20240716_JN_SLEscRNA
workDir : /mnt/Extend1/leiyao/20240716_JN_SLEscRNA/work
projectDir : /home/leiyao/.nextflow/assets/nf-core/scrnaseq
userName : leiyao
profile : singularity
configFiles :
Input/output options
input : samplesheet.csv
outdir : ./Result
Mandatory arguments
aligner : cellranger
protocol : 10XV2
Reference genome options
fasta : ./Data/Homo_sapiens.GRCh38.dna.toplevel.fa
gtf : ./Data/Homo_sapiens.GRCh38.112.gtf
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/scrnaseq for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.3568187
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/scrnaseq/blob/master/CITATIONS.md
------------------------------------------------------
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC -
executor > local (1)
executor > local (2)
executor > local (5)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
executor > local (5)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
executor > local (9)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
[12/ed39cd] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[9a/ac459f] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKGTF (Homo_sapiens.GRCh38.dna.toplevel_genes.gtf) [100%] 1 of 1 ✔
[ac/24f578] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[77/62a987] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (L01_3) [100%] 1 of 1 ✔
[21/06b153] process > NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3) [ 0%] 0 of 1
[46/3f7020] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (L01_3) [100%] 2 of 2
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD -
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT -
[84/804f99] process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC [100%] 1 of 1 ✔
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)` terminated with an error exit status (1)
Command executed:
mkdir emptydrops_filtered/
emptydrops_cell_calling.R \
matrix.mtx.gz \
barcodes.tsv.gz \
features.tsv.gz \
emptydrops_filtered \
cellranger \
0
Command exit status:
1
Command output:
[1] "Only kallisto and alevin have transposed matrices."
Command error:
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
executor > local (9)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
[12/ed39cd] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[9a/ac459f] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKGTF (Homo_sapiens.GRCh38.dna.toplevel_genes.gtf) [100%] 1 of 1 ✔
[ac/24f578] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[77/62a987] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (L01_3) [100%] 1 of 1 ✔
[21/06b153] process > NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3) [100%] 1 of 1, failed: 1 ✘
[46/3f7020] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (L01_3) [100%] 2 of 2 ✔
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD -
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT -
[84/804f99] process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)` terminated with an error exit status (1)
Command executed:
mkdir emptydrops_filtered/
emptydrops_cell_calling.R \
matrix.mtx.gz \
barcodes.tsv.gz \
features.tsv.gz \
emptydrops_filtered \
cellranger \
0
Command exit status:
1
Command output:
[1] "Only kallisto and alevin have transposed matrices."
Command error:
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
executor > local (9)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
[12/ed39cd] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[9a/ac459f] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKGTF (Homo_sapiens.GRCh38.dna.toplevel_genes.gtf) [100%] 1 of 1 ✔
[ac/24f578] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[77/62a987] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (L01_3) [100%] 1 of 1 ✔
[21/06b153] process > NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3) [100%] 1 of 1, failed: 1 ✘
[46/3f7020] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (L01_3) [100%] 2 of 2 ✔
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD [ 0%] 0 of 2
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT -
[84/804f99] process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/scrnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)` terminated with an error exit status (1)
Command executed:
mkdir emptydrops_filtered/
emptydrops_cell_calling.R \
matrix.mtx.gz \
barcodes.tsv.gz \
features.tsv.gz \
emptydrops_filtered \
cellranger \
0
Command exit status:
1
Command output:
[1] "Only kallisto and alevin have transposed matrices."
Command error:
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
executor > local (9)
[9c/23caad] process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (L01_3) [100%] 1 of 1 ✔
[12/ed39cd] process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[9a/ac459f] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKGTF (Homo_sapiens.GRCh38.dna.toplevel_genes.gtf) [100%] 1 of 1 ✔
[ac/24f578] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.toplevel.fa) [100%] 1 of 1 ✔
[77/62a987] process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (L01_3) [100%] 1 of 1 ✔
[21/06b153] process > NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3) [100%] 1 of 1, failed: 1 ✘
[46/3f7020] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (L01_3) [100%] 2 of 2 ✔
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD [ 0%] 0 of 2
[- ] process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_SEURAT -
[84/804f99] process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/scrnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:EMPTYDROPS_CELL_CALLING (L01_3)` terminated with an error exit status (1)
Command executed:
mkdir emptydrops_filtered/
emptydrops_cell_calling.R \
matrix.mtx.gz \
barcodes.tsv.gz \
features.tsv.gz \
emptydrops_filtered \
cellranger \
0
Command exit status:
1
Command output:
[1] "Only kallisto and alevin have transposed matrices."
Command error:
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
[1] "Only kallisto and alevin have transposed matrices."
Error in .local(m, ...) :
insufficient unique points for computing knee/inflection points
Calls: emptyDrops ... .local -> do.call -> <Anonymous> -> <Anonymous> -> .local
Execution halted
Work dir:
/mnt/Extend1/leiyao/20240716_JN_SLEscRNA/work/21/06b153ef96a6515ec7073a1c6773c6
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
Description of the bug
The error appear when nf-core/scrnaseq is launched with any aligner at the emptydrop step. The pipeline is labelled as completed but with errors as it failed with the output error : "Only kallisto and alevin have transposed matrices."
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version 24.04.3 Hardware Desktop Executor local Container engine Docker Os Ubuntu Version of nf-core/scrnaseq v2.7.0